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. 2021 Apr 1;184(7):1706–1723.e24. doi: 10.1016/j.cell.2021.02.040

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© 2021 The Authors

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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Figure S4 — Haplotype-based analyses and estimates of effective population size variation over time, related to Figure 3

(A) The PCA was built using copying vectors inferred using a modified version of ChromoPainter that allows for the presence of missing data. The masked individuals (rmIA311) have been projected on the variability of the nearly unadmixed individuals (uIA217) regardless of the level of missing data. The unadmixed individuals are indicated with full filled dots while the masked ones are represented by different shapes, according to the percentage of missing SNPs. The colors refer to the clusters (donors) of Figure 3A. (B) Heatmap based on individual TVD (Total Variation Distance) values. Dendrogram branches are colored according to 19 clusters (Figure 3A). The TVD was compared both among and within clusters. Lighter colors (lower TVD values) in the matrix mean similarity, while darker colors (higher TVD values) indicate heterogeneity.

(C) We used RefinedIBD on inferred IBD length to estimate variations in the effective population size (Ne, on a log scale y axis) over time. The x-axes show the time before the present as years ago (ya) considering a generation time of 25 years and the colored regions show 95% bootstrap confidence intervals (CI). The analyses were limited to the last ~2,000 years, due to the wide variance of exponentially distributed IBD fragments and were performed on different datasets. The Guna group was evaluated considering different IBD thresholds (2 cM, 4 cM and 6 cM). (D) We double-checked the trend presented in the inset of Figure 3C without the Guna. (E) We also compared the IBDne of the Panamanian macro-clusters with the others identified in Figure 3A, Western Panama: Western Isthmus, PaNASO, PaNGABE; Emberà: PaEMBERA; Guna: PaGUNA; Colombia KCH: Colombia, Ecuador (KCH); South America Peru: SouthAmerica1, SouthAmerica2, Peru North Coast, SouthAmerica3; North Central Mexico: Central America, North America, Mexico; Brazil all: Brazil, Xavante, Karitiana, Surui, Guarani. (F) Visualization of the average of summed IBD lengths shared between modern Panamanians and other IA populations in each paired comparison, with identified IBD blocks in the range of 1–5 cM (oldest), 5–10 cM, and over 10 cM (youngest). Shape sizes are proportional to mean values; only those pairs sharing at least two blocks > 5 cM and four < 5 cM are plotted.